The Pocket AVR Programmer is just a standard ISP programmer, meaning it uses the ISP protocol built into the hardware of the microcontroller to write data to flash and EEPROM. That is also the way, that the bootloader got onto the microcontroller in the first place.
The bootloader of the Arduino on the other hand is a small program to communicate over Serial (or USB depending on the Arduino board) and then write the data to flash and EEPROM.
So: No, you don't need the bootloader, if you want to use the ISP programmer. Select your programmer in the corresponding menu of the Arduino IDE to use it.
Though keep in mind, that you won't be able to upload a new sketch via Serial/USB without the bootloader. You can always use the ISP programmer to again write the bootloader to the microcontroller.